


Amelia

by RegalPotato



Category: Doctor Who, Doctor Who (2005)
Genre: Angst, F/M, Hurt/Comfort, Time Babies
Language: English
Status: Completed
Published: 2017-01-07
Updated: 2017-01-10
Packaged: 2018-09-15 09:43:31
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 5
Words: 10,720
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/9229154
Author URL: https://archiveofourown.org/users/RegalPotato/pseuds/RegalPotato
Summary: When the TARDIS sends them spiraling into a gun fight, the Doctor gets thrown into a whole heap of spoilers he really has no business being involved in.





	1. Chapter 1

**Author's Note:**

> I wrote this around four years ago? So it's not the greatest thing ever, but it's finished and I spent time writing it (I don't know why I never posted it, I think I was too worried because this fandom has some amazing fic writers and I don't feel worthy). Anyway, enjoy.
> 
> Time Line: Post Berlin (LKH) for the Doctor and the Ponds (but before TWoRS) and somewhere just after she's been pardoned (but before she's a Professor) for River.

“So, where to next?” The Doctor asked gleefully. He began bounding around the TARDIS console, flipping switches which River casually unflipped and pressing buttons that River nonchalantly unpressed.

“Space Florida again.” 

“Somewhere not dangerous.” 

“Or maybe Ancient Rome.” Amy winked at Rory.

“Or maybe somewhere not dangerous,” the ex-Roman repeated. 

“Or maybe…” Amy trailed off as the TARDIS suddenly began to shake violently, sending all four occupants ungracefully to the floor.

“What the…?” The Doctor muttered, jumping up and grabbing the TARDIS’ scanner.

River appeared next to him, grabbing the scanner herself and inputting a few commands. The Doctor huffed, but turned his attention to trying to stabilise the TARDIS as another jolt almost sent everyone flying.

“What’s going on?” Rory asked. 

He stumbled upright, and helped Amy off the floor. 

“She’s pulling us off course and out of the time vortex,” River shouted. She slammed her hand down on the blue stabilisers, but to no avail. “Something must have seriously upset her.”

They all fought to remain standing, holding onto the console with all their strength as the TARDIS shook around them. Both River and the Doctor danced around Rory and Amy, and each other, pulling levers and turning dials in no particular sequence.

“Nothing’s working,” River gasped after a particularly nasty shake caused her hip to collide with the console. 

“I know, I know,” the Doctor yelled, waving his arms manically, sonic screwdriver in one hand and frustration evident on his face.

Suddenly there was an ear wrenching screech and the TARDIS shuddered before all motion stopped. Everyone took a moment to right themselves, and the Doctor stroked the TARDIS console gently, muttering to her.

Amy was the first to speak aloud. “I think I'm going to be sick.”

Rory agreed, both Ponds looking paler than usual.

“Where are we? _When_ are we?” River asked as the Doctor grabbed the scanner.

“51st Century, a small planet on the edge of the Kloix system…” the Doctor replied, intrigue lacing his voice.

His confusion suddenly morphed into joy and the Doctor bounced over to the TARDIS doors. “I do love a mystery. Coming?”

And with that he vanished outside.

Amy looked at Rory, a smile forming as the colour flooded back to her face. She grabbed her husband and pulled him after the Doctor, ignoring his suffering sigh and mutter of “this isn’t going to be somewhere safe”.

River patted the TARDIS console, murmuring words of comfort just like the Doctor had. Something didn’t feel quite right. There wasn’t much that could wrench the TARDIS out of the vortex. Her fingers fluttered over her gun strapped to her waist, subconsciously checking it was still there. 

“Coming, Doctor Song?” The Doctor’s head popped back through the doors, a large welcoming grin spanning his face.

River ignored the sense of wrong, pushing it away. She forced herself to grin back at the Doctor and jogged down the stairs after him.

The TARDIS had landed them in the middle of a rainforest. The air was heavy and humid, and sounds of alien bird call echoed in the distance. It was eerily dark, the thick canopy above them blocking out most of the planet’s sun. 

“Why’d the TARDIS bring us here?” Amy asked no one in particular.

Before anyone could answer, not that anyone knew what the answer was, shouts and screams, followed by the sound of old fashion gun shots cut through the rainforest. A young woman came bursting through the tree line. She looked to be early twenties, and she was covered in mud; her blond hair was dirtied brown and her clothes were torn and bloodied. Beside him, the Doctor heard River gasp. 

The woman’s eyes lit up in relief as she spotted the TARDIS and the group stood in front of it. She ran towards the shocked foursome, pressing a button on the device strapped to her arm.

“It worked. He’s here,” she managed to yell above the noise behind her.

However, just before she reached the Doctor and his companions, the girl’s face morphed into confusion and then shock before finally contorting into pain. She fell forwards heavily, landing at River’s feet. Rory jumped into action and bent down to help the girl as soon as he noticed the large red circle appearing on the woman’s back.

“She’s been shot,” he explained unnecessarily, checking the woman’s pulse before gently rolling her over and to check her breathing. “Help me get her in the TARDIS.”

Amy crouched down next to her husband and grabbed one of the woman’s arms. The two of them stumbled towards the TARDIS with the woman between them. The Doctor turned and shouted to the pair, telling them to take her to the medical room. He missed the look of horrified concern that passed across River’s features as watched the woman disappear into the Police Box. 

“Put it away, River,” he demanded without even looking at her.

River ignored him and kept her gun pointed at the tree line. The foliage rustled and River aimed the gun slightly higher as a man came blundering through the leaves. 

“Captain?”

“Jack?” 

Both River and the Doctor exclaimed at once, the Doctor’s expression one of surprise, River’s one of anger.

“In the TARDIS!” He yelled, running straight past them both and into the Police Box. River looked at the Doctor, who had turned his head back to the trees. 

“I’ll kill…shoot him,” she growled.

He was about to ask why, and how she knew the captain in the first place, when a group of angry looking men burst into view. Sighing, River grabbed the Doctor and pulled him into the TARDIS, shooting warning shots above the men to cover their escape.

As soon as the doors slammed behind them, the Doctor was at the controls attempting to send them spinning into the time vortex. He turned around, expecting to see River correcting his every move, and was surprised and slightly disappointed - though he’d never in a million years admit it – to see her disappearing down the corridor towards the medical room.

Once he knew they were safe in the vortex, having had enough of the intrigue and wanting some answers, the Doctor rushed to the medical room. He entered the room just in time to see River shoot Jack in the chest with her blaster at point blank range. Amy and Rory both screamed, the latter dropping down to check Jack’s pulse.

“What’d he do this time?” The Doctor asked her casually, surprised at her reaction to the Torchwood agent.

“What the hell, River?” Amy screamed as Rory announced the man dead, horrified at her daughter’s callousness. 

River ignored Amy, jamming her blaster back into its holster and moving closer to the woman on the medical table. Rory had quickly removed the bullet, which had fortunately missed all the woman’s vital organs. He’d also stitched her up and bandaged her. River gently brushed the woman’s dirty hair from her face.

The Ponds both jumped, shocked into silence, when Jack gasped back to life. He breathed deeply for a few moments before staggering to his feet, perfectly fine apart from the hole singed into the front of his shirt. 

“Jeez, Song,” Jack muttered, rubbing the non-existent wound on his chest. 

River furiously spun on the ex-time agent, gun once again aimed at his torso. But the Doctor was quicker, grabbing her arm gently, and slowly prying the gun from her grip. Once he’d removed the gun, he chucked it on an empty medical table behind him. The Doctor turned to face Jack, hand still wrapped around River’s. 

“Okay, I think we all need to calm down,” he spoke gently, squeezing River’s hand affectionately. “Ponds, before you ask, this is Captain Jack Harkness. He’s immortal. Can’t die. Long story. And Jack, before I ask, tell me what’s going on.”

Jack was spared having to tell anyone anything by the small moan that came from the woman on the medical table. A bright light suddenly exploded from her causing the five other occupants of the room to step away and cover their eyes. 

“What was that?” Amy asked after the light faded, having finally found her voice.

“It looked like when the TARDIS left her body,” Rory said slowly. “Almost like regeneration…”

“River?” The Doctor turned on her, facial features stretched between anger and confusion. “Care to explain why this girl just used time energy to heal herself?”

River smiled weakly, pausing to throw a glare in Jack’s direction.

“Spoilers?” She winced, lacking in her usual confidence as the Doctor’s face darkened. “Doctor, this is….”

A weak voice coughed from the medical table. “Whatever she says, I prefer Lia.”

River ignored the stares from the Doctor and her parents and rushed to Lia’s side. She brushed the woman’s hair back from her face, checking her over for any residual effects of using the time energy.

“I’m fine,” she coughed.

When River verified that Lia was in fact fine, her worried features turned livid. 

“What were you thinking?”

Jack carefully pulled the archaeologist away from Lia as the girl’s eyes fluttered sleepily. 

“Let her rest, Song.”

River span round to face Jack, fury etched over her face. The captain’s usually charming smirk faltered, his skin tone became several shades paler as he backed up to hide behind the two confused Ponds. Feeling the need to protect him, the Doctor gently grabbed River’s arms, preventing her from reaching Jack.

“Okay, I think some of us need an explanation. Jack why aren’t you at Torchwood?” The Doctor asked.

“Doing some freelancing. Gwen’s got everything covered back in Cardiff.” 

“And Lia?”

“She works with us at Torchwood…”

“Like hell she does!” River spat.

“It was her choice, Doctor Song. I didn’t force her.”

“No but I bet you did a damn good job of convincing her!”

“Hold it!” Amy stepped forwards, preventing Jack from retorting. “Who is Lia?”

Jack’s eyes met River’s. “Oh great, you just had to bring the wrong versions of them.”

“Me? The TARDIS brought us here. You promised she’d be safe. I had no idea you’d be dragging her across the universe.” River pushed herself out of the Doctor’s grasp.

She strode up to Jack and grabbed a fistful of his shirt. “Do you know what would happen if someone got to her? Do you really want the weight of that on your shoulders, Captain?”

“Okay that’s enough.” The Doctor moved to the centre of the room, separating the two. “Amy, Rory could you stay and look after Lia please. River, Jack, with me. Now.”

The Doctor headed to the control room, River and Jack following in silence. He casually leant against the console before levelling his gaze at River.

“I can’t tell you.” She swallowed heavily, pre-empting the Doctor’s questions. “All you need to know is that she should currently be locked deep inside Torchwood. She’s meant to be safe.”

“Who is she?” River remained silent. “River, tell me what’s going on. If I’m going to help, I need to know.”

River paused for a moment, before closing her eyes and breathing deeply. “She’s…she’s someone very important to me. And that should be more than enough knowledge for you to help me.”

Silence stretched across the room. The Doctor’s head was swimming with too many thoughts. Jack sighed.

“You don’t know what all this will do to the timeline,” he said.

“Oh, yes this is all _my_ fault,” River deadpanned. “And I know very well what could happen to the timeline.”

“Actually, where are you in your timeline?” Jack asked the Doctor, turning to ignore River.

“Um, we did Berlin about a month ago.” 

“Oh good, so at least we’re at the stage where you two are together…”

Jack trailed off as he saw the horrified looks on both their faces. River buried her face in her hands as the Doctor sat up straight against the console.

“Oh dear God, woman. You really need to sort your timeline out.”

“God dammit, Harkness!” River ripped her hands down from her face. 

“River, I…” The Doctor started, stopping River from harming Jack again.

“Don’t. Please Doctor, just stop. The rules are there for a reason.” River’s voice was tight with frustration.

“Screw the rules, River. Stop with all the bloody secrets!” 

“You think I have a choice? I would love nothing more than to be able tell you everything. Everything about us, about Lia, about your future. But if I do, it might not happen.” River’s eyes began to shine with unshed tears. “I’d rather you hate me now if it means I don’t rewrite all that.”

The Doctor was still angry, but Jack stepped between the two of them, instantly siding with River. His mouth was set in a stern frown, his stance protective.

The Doctor raised his eyebrows, staring angrily at River over Jack’s shoulder. Without a word, River spun around and left the console room. The Doctor’s stance sagged a little as he noticed River bringing a hand up to wipe at her eyes as she left.

“God, I can’t do anything right, Jack,” the Doctor muttered.

“Do you love her…?” He asked, only just managing to stop himself adding ‘yet’ to the end of the question.

The Doctor sighed and slumped against the TARDIS console. He nodded slowly, muttering “I think so” before suddenly smacking himself in the head. 

“I’m so _stupid_. But she drives me insane.”

“Isn’t that a good thing?” Jack smirked.

The Doctor rolled his eyes.

“I still don’t know who she is, who she really is, or who she kills. She’s Amy and Rory’s daughter, is practically a Time Lord. But who is she to _me_?” The Doctor looked at Jack, practically begging him for the answers.

“If you haven’t figured that out by now, you’re not the genius you say you are.” Jack’s smirk remained. As he sauntered out of the control room, leaving the Doctor to his thoughts, he threw a wink over his shoulder. “And if I were you, I wouldn’t complain about having River Song driving you insane.”


	2. Chapter 2

It was a few hours later when the Doctor had finally decided to seek River out. Jack had fallen asleep watching over the still sleeping Lia, and Amy and Rory had retired to their bedroom. The Doctor was pretty sure the TARDIS was angry at him. He’d looked for his study for over an hour before giving up and admitting defeat. 

“Okay, I get it. Just let me find her now so I can apologise please,” he shouted at the ceiling.

He turned the corner and the door to his study finally appeared in front of him. He smiled, silently thanking the TARDIS, even though he felt slightly betrayed that she’d taken River’s side on the matter. Slowly turning the handle, he slipped into the dark room. It wasn’t difficult to find her. River was curled up on the large comfy chair in the middle of the room. Her hair was sprawled over her face, but the Doctor could tell by her breathing that she was fast asleep. Her battered diary lay forgotten on her lap. 

Once again the Doctor shook himself for his stupidity. He knew none of this was River’s fault. In fact her entire life was entirely down to him. The guilt for that, and for yelling at her, tore at him briefly before he got back to the moment at hand. 

He carefully tucked River’s diary into his pocket before moving to pick her up. He swallowed thickly as he noticed how easily she fit against him and his breath caught in his throat as River snuggled into him, trusting him completely even in her sleep. Silently he left his study. He was entirely sure River had a room on his TARDIS, though he’d never seen it, but instead of looking for it, he opted for his own bedroom. He quickly found his door, the TARDIS obviously deciding to help out, and managed to open it without dropping the sleeping woman in his arms. 

The Doctor gently placed River on his bed. He then stood for a moment, fidgeting nervously at whether to remove her clothes or not. In the end, he removed her boots and her jacket then pulled the bed covers over her. Most people looked peaceful when they slept, but the Doctor had to once again force down his overwhelming guilt as he looked at River’s face and noticed the discomfort she displayed.

He turned to leave but stopped suddenly when he heard River whimper. He breathed in deeply before turning round and walking back over to her, crouching down beside her and softly moving her hair from her face. His hearts almost stopped when he heard her whisper his name in her sleep. Not ‘Doctor’, but his actual name.

Ever since he met her, the Doctor knew at one point he’d tell this woman his true name. In The Library, hearing it brought about confusion and a soft amount of anger, but hearing her whisper it now as she slept made his hearts melt in his chest. All thoughts of leaving her to sleep by herself vanished from his mind. The Doctor quickly placed her diary on the nightstand next to the bed before stripping out of his tweed jacket and toeing off his shoes. As quietly as he could, he slipped into the bed beside River. He lay there awkwardly for a moment or two, but then River turned in her sleep and cuddled into him. The Doctor lay still, not breathing for a moment. Then his brain slowly started to register River’s soft, contented breathing against him and he relaxed into the bed. 

He hardly ever slept, but with River lying against him the Doctor found himself rather exhausted and his eyes slowly fluttered shut, sleep encasing him.

-

River woke feeling quite uncomfortable. Moving slightly she noticed she was still fully clothed. She frowned slightly, not remembering going to sleep in her bed last night, and her frown only deepened when she suddenly noticed the Doctor was also fully clothed and sleeping soundly beside her. Her frown quickly vanished into a soft smile as the Doctor pulled her closer in his sleep. She turned her head to face his.

“Time to wake up, Sweetie,” she whispered against his ear.

The Doctor groaned childishly and River swore she heard him mutter “five more minutes”. She rolled her eyes, getting out of bed and rifling around in the dresser for fresh clothes for the day. Her shuffling gradually brought the Doctor out of his hazy sleep and he blinked heavily, his eyes focusing on the woman searching through his clothes drawers.

“What are you doing?” He asked, all flustered.

“Getting changed, what does it look like?” 

“But, but…this is my bedroom. How do you have clothes in here?”

River suddenly froze. The events of the past few days, especially the previous day, flooded back to her. It hit her hard when she remembered this wasn’t _her_ Doctor or _their_ bedroom. She looked into the open drawer in front of her, noticing her neatly laid out clothes - bless the TARDIS - and then slammed the drawer shut.

“I don’t. Was just being nosey.” River grinned, the flirty lie slipping far too easily through her lips. “I’m just going to go change in the TARDIS wardrobe.”

She smiled, it was forced but thankfully – or hurtfully, depending on whose view you took – the Doctor didn’t notice her deception. Forcing back tears that were coming far too easily recently, at a time where her Doctor was starting to forget who she was, River grabbed her diary and slipped out of what used to be their bedroom, but now was solely his.

-

The Doctor shook his head as he strolled into the medical bay. River’s strange behaviour this morning confused him. Maybe it was waking up next to him, but he knew it wasn’t as simple as that. 

“Good morning, Jack.” The Doctor beamed.

Jack stirred groggily from the chair he’d fallen asleep in. He groaned slightly, stretching his arms and rolling his shoulders.

“Morning, Doc.” 

“How is she?” The Doctor asked, referring to the sleeping girl on the medical table.

“Stable. The time energy from yesterday…” Jack paused slightly at the sensitive topic. “Well, she’s fully healed and should be waking up from the exhaustion any time soon.”

The Doctor nodded quietly, deep in thought.

“Who is she Jack?” Jack opened his mouth to reply but the Doctor interrupted him. “How do you and River even know each other anyway?”

“She’s accidentally got me out of a few tough situations in the past,” Jack answered vaguely. “And Torchwood’s the best place for her to hide A….Lia.”

The Doctor noticed Jack’s almost slip up, but chose to ignore it for the moment. He strode around to the other side of the medical table and looked intently at the girl.

“How did she heal herself?” The Doctor asked himself more than Jack.

He flipped open his sonic screwdriver.

“Doctor, wait.” 

The Doctor faltered at Jack’s outburst, eyebrow raised. Jack paused, not actually knowing what to say to stop the Time Lord from scanning the girl on the medical table. Thankfully, he didn’t have to think of an excuse as Amy’s shouts from the control room filtered into the medical bay. With a quick look at Jack, the Doctor rushed out of the room.

Jack sighed and slumped back into the chair he’d used as a bed for the night. Lia began to stir and her eyes flickered open.

“Morning beautiful.” Jack shot her a flirty grin.

Lia sat up slowly, and scratched absently at where her bandages had once been. When she noticed Jack, she beamed brightly at him.

“We’re on the TARDIS?” She asked gleefully.

Jack laughed before his face turned serious. He had a lot of explaining to do. 

-

The Doctor entered the room and bounded over to the console. Rory pointed at the scanner which was glaring bright red, a signal weaving its way across the screen. The Doctor grabbed the scanner just as Jack walked into the room, Lia supported on his arms.

River entered from below the console platform, having changed into a white shirt and dark trousers. He smirked when he noticed they were jodhpurs. She silently made her way to Lia’s side and the Doctor turned back to the scanner, slapping it when the screen fuzzed out momentarily.

“What is it?” River asked.

“A signal…” 

“Well we can see that.” Amy rolled her eyes.

“A signal that shouldn’t be making its way into the TARDIS,” the Doctor continued.

River squeezed Lia’s arm before making her way towards the Doctor. She grabbed the scanner from him, spinning it round to get a better view of it.

“It’s a tracking signal,” she thought aloud, speaking before the Doctor had a chance to huff at her. “Something, or some _one_ , on the TARDIS is under surveillance. And someone is tracing where they are…across the whole universe.”

There was silence for a moment.

“Right!” The Doctor shouted, causing the majority of the group to jump. “Arms out, legs spread. Someone’s bugged and we’re going to find out who.”

“Hold on, if they can bug someone on the TARDIS do you really think your screwdriver will work?” 

The Doctor span round to face Lia as she spoke. Her voice was light, but just like his own, contained a depth of sadness to it. As he turned to her, she smiled a little uneasily. He held his sonic screwdriver out, ready to scan her before it was suddenly grabbed out of his hand by River.

“River!”

River smirked. 

“Until you can behave, which means not scanning people without their permission,” River paused as the Doctor tried to interrupt. “Don’t deny it, dear. It’s rude. Until then, I’ll look after this for you.”

She quickly scanned Lia, her smile falling as the sonic beeped.

“It’s Lia…” Jack trailed off.

The Doctor made to grab his screwdriver back, but River tucked it into the back of her trousers causing the Doctor to splutter indignantly.

“And to think I was looking forward to you having to frisk me,” she joked with a wink.

Jack smirked as Amy rolled her eyes and Lia pulled a disgusted face at River’s actions. The Doctor also coughed awkwardly, quickly turning back to the scanner to hide his blush. 

“Right, so someone’s tracking Lia. Their technology is good enough to penetrate the shields around the TARDIS but…AH HAH!”

The scanner beeped. 

“But it isn’t good enough to stop me reversing the signal and tracing it right back to them.”

The Doctor grinned, flipping a switch on the TARDIS, sending them flying towards the origin of the signal.

-

They stepped out of the TARDIS into a dark, spacious warehouse. Wooden boxes and metal crates were scattered in no particular order throughout the room. River raised her handheld computer to scan for the signal that had infiltrated the TARDIS.

“Something’s jamming it.” River frowned, tapping her device slightly with her hand.

The Doctor went to reach into his jacket for his sonic before realising River still had it. 

“River…” The Doctor pointed towards his screwdriver.

River raised her eyebrow and the Doctor winced as he realised he was also pointing towards River’s bum. 

“Just scan.” He sulked, arms flailing slightly.

She grinned and flipped out his sonic to scan the area. No sooner had the green light buzzed, all hell broke loose. A variety of different coloured plasma rounds pierced the air only just failing to drown out orders shouted across the warehouse.

“It’s a trap!” Rory yelled, grabbing Amy and pulling her behind him.

A plasma bolt shot through the air, only narrowly missing the Doctor. He sighed in relief as it flew past him. His relief, however, was short lived as River screamed.

“Amelia!” 

The Doctor span round almost in slow motion, hearts in his throat and fully expecting to see Amy’s lifeless body fall into Rory’s arms. His mouth fell open in shock when instead he watched Lia’s body fall to the floor, a large black burn mark singed across her chest. River was on the floor in seconds, knees crashing to the ground beside the girl. Jack mirrored her actions. 

Amy was screaming at the Doctor to do something and Rory was trying to stop Amy from getting herself killed. Plasma rounds still filled the air, everyone’s voices merged into one and when a round passed close enough to River to singe her hair, though she didn't even notice, the Doctor exploded.

“STOP IT!” He yelled and magically, unexpectedly, everything slowed to a silent stop.

“I don’t know who you are and I don’t know what you want, but you should know not to mess with me. I’ve seen thousands of worlds burn, sometimes at my own hands, and I’ve seen hundreds of civilisations destroy themselves. Daleks dread me; Cybermen fear to use me, and even the Vashta Nerada run at the mention of my name,” the Doctor paused. “If there is one thing you do not want, one thing that’ll mean the end of your race, or your species, or your world, it’s becoming an enemy of the Doctor.”

There was a fearful silence for a moment, before the sound of dozens of feet shuffling, retreating, could be heard. Suddenly a single man stood out from behind a large metal crate next to the Doctor. River was upright in an instant, blaster in her hand. The Doctor held up his hand, walking closer to River so her view of the man was obscured.

“Who are you?” The Doctor asked.

“We’re mercenaries,” the man, an ordinary human by the Doctor’s calculations, answered with a gruff voice.

He was wearing metal plated armour that was patched together from different makes and models and had obviously seen better days. Held loosely in his hands was a large 51st Century plasma rifle.

“What do you want?” River said, her voice icily calm; something that had the Doctor on edge.

“Some religious nutters paid us to capture the girl. It looks like we won’t be getting our bounty after all. They did say preferably alive than dead.” The man frowned, nodding towards Lia’s still body. “But they mentioned nothing about the Doctor being with her.”

“Who’s paying you?” River asked, her gun not wavering even though she didn’t have a clear shot.

“The Silence.” 

Everyone gasped and the Doctor whirled around to face Jack, still keeping himself between River and the mercenary. 

“Jack, take Lia back to the TARDIS. Rory, take Amy and go with Jack,” the Doctor ordered.

“What about River?” Jack asked, gently picking Lia up with Rory’s help.

“We all know she doesn’t listen to me.” The Doctor grinned, sending a flirtatious wink in River’s direction.

The corner of River’s mouth lifted in a half smirk at the Doctor’s comment, but her eyes didn’t waver from the mercenary. 

“Why do they want the girl?” The Doctor pressed on, spinning on his heels to turn back to the mercenary.

The Doctor’s hand slowly came up behind him to grasp River’s spare one, squeezing it slightly.

“Hell if I know. Listen man, take the girl and go. Fighting _The Mighty Warrior_ isn’t something we signed up for. Just leave.”

And with that the mercenary turned and fled.

The Doctor sighed, wincing at the term the mercenary had used. River tugged at his hand, her face a blank mask as he looked up at her. 

“Come on, my love. Let’s get out of here.”

River raced back into the TARDIS, barely checking to see if the Doctor was following her. Once again, River disappeared down the corridor towards the medical bay.

“Who are you Amelia?” The Doctor pondered out loud, knowing there was more to her than just the obviousness of her name.


	3. Chapter 3

Four hours later, the TARDIS safely parked in the visitors’ area of the Sisters of the Infinite Schism, the Doctor found River in his study again. She was curled up on the same chair he’d found her on the previous night only this time she was awake. Her eyes were glazed over and it looked like she’d been staring at the wall for hours.

“River…”

She didn’t turn to face him, or even acknowledge his presence in anyway, and when he looked at her and saw the familiar eyes of a worried parent, something finally clicked in his head.

“Oh god. Oh River, I’m sorry. I’m so, so sorry.” He crouched down in front of her and grasped both her hands with his.

She finally looked at him then.

“I really need you,” she whispered, forcing back the tears that threatened to fall.

“I’m here, River.”

“No. Not you,” she hissed, instantly regretting her tone when the Doctor flinched. “I…I need _you_. My Doctor. The one who knows who I am.”

“I wish I could be him, River. But I’m not. Not yet.” The Doctor’s voice was soft and he let his forehead rest against their joined hands.

“Her heart isn’t strong enough.” River changed the subject suddenly. “The plasma blast tore straight through her chest, badly damaging her heart. It’s too weak for her body to heal itself.”

The Doctor’s hands tightened around hers, his forehead pushing harder against the back of his hand.

“She’s going to die, Doctor. And you don’t even…” She choked back a sob.

“River. River listen to me. She’s not going to die.”

He pulled her up out of the chair and into his arms. She clung to him like a lifeline and with a sudden shock, as if ice cold water had been thrown over him, the Doctor suddenly realised he’d never hugged River before. He held her all the tighter because of it.

“She’s not going to die, River. I’ll rewrite time if I need to.”

River gasped into his chest, bringing her eyes up to meet his. He answered her before she even got a chance to voice her question.

“Because she’s your daughter, River. That’s the only excuse I need.”

She kissed him then, suddenly and without warning. Her hands gripped his back tightly and her tongue invaded his mouth. The Doctor fought down the urge to flail, moving one hand to her lower back and bringing the other up to run through her hair. Her teeth tore at his lip and he whimpered slightly into her mouth.

An awkward cough sounded from the study’s entrance and the Doctor jumped, quickly disentangling himself from River, his face bright red.

“Sorry to interrupt,” Jack’s face was solemn. “But I need to talk to you, Song.”

“Captain, whatever it is…”

“In private,” he stressed, turning from the room.

River looked up at the Doctor who stood next to her uncomfortably. 

“Thank you, Sweetie.” Her hand rested on his cheek for a moment and then she turned to follow Jack.

As soon as she left, the Doctor collapsed into the chair River had been in only minutes earlier. He ran a hand over his face and sighed. His eyes glanced towards the study door and he licked his lips in thought, pausing when he tasted River on them. With a frown he stood up and inched towards the door.

“She needs a new heart. The Sisters said it was the only way for her to live.” He could hear Jack’s muffled voice fading down the hallway. "They can keep her alive indefinitely, but only in a comatose state." 

He cracked open the door.

“She can’t just have any heart though, Jack. You and I both know that. A normal human heart would just be eaten up by the time energy inside her.” He could hear them clearer now; River’s voice was on the verge of tears.

“They said her father…”

“No.” The Doctor heard Jack sigh at River’s curt dismissal. 

“River, just let me do it.”

The rest of the conversation drained into background noise as the blood pumping through the Doctor’s ears grew louder.

Jack Harkness was Lia’s father. 

_Jack Harkness_ was River Song’s daughter’s father.

The Doctor felt sick. His brain shut down. He slammed the door shut and slid down it, head falling into his hands. He didn’t know what he was expecting, though he knew what he’d hoped.

He never heard the end of the conversation.

“I’m not letting you do it either, Jack.”

“Listen, it makes more sense for me to do it than him anyway. It’d be much more risky for him. Me? You can’t kill me.” He winked but River knew his flirtatious charm was just covering up how terrified he felt. “They can take out my heart. I’ll die. But I’ll just grow a new one. I’m immortal. My heart should be too right?” 

River almost screamed in frustration at how obvious yet dangerous the solution was. Instead, she pulled out her blaster and shot Jack squarely in the chest.

“I appreciate the sentiment, Jack,” she started sweetly as the Captain gasped back to life. “But this is your fault in the first place. She should still be inside Torchwood.”

Jack grimaced and stood up, muttering about how dying still hurt and the number of shirts he needed when River was around. 

“You should know what it’s like to be caged, River Song. And with you and him for parents, did you think I really had a choice in keeping her there.”

He turned away from her.

“And I’m doing this. This time I do have a choice.”

And with that, he left River standing dumbly in the corridor. 

-

Rory didn't know what was going on. Oh he could make quite a few guesses but he didn't think he'd quite get it right. He was sitting in a hospital room, not unlike the one they'd left River in a month ago. Amy was sat on the other side of the hospital bed, hand grasped around Lia's cold and pale one. 

"I don't get it." Rory finally gave up guessing, silently asking Amy to explain it to him.

"The way River explained it to me," Amy paused. "Is that Lia can't regenerate. She only has one heart instead of two and so uses whatever Time Lords use, to heal herself instead. But because she's only got one heart..."

"It's not strong enough to fix serious damage," the Doctor finished for her as he walked into the room. "She's River's daughter."

"We know. River told us." Amy turned back to Lia. "She's our granddaughter. God I feel old."

Amy laughed, but it was forced. Rory felt his own pain at their situation escape from the room he carefully kept locked in his mind. A daughter older than them, a granddaughter almost the same age as them. No chance at seeing either of them grow up. And now Lia's life was hanging in the balance. 

He was old. Over 2000 years old. And the pain never got easier to deal with.

"I..." The Doctor trailed off, not knowing what to say, not even knowing why he was there.

He stood at the foot of the hospital bed and just stared down at Lia, a mix of unreadable emotions crossing his face. Amy smiled sadly. She squeezed Lia's unmoving hand and gestured to Rory for them to leave. Rory squeezed the Doctor's shoulder as he passed. 

"You've got human plus DNA in you. I get that. But why are you so important to them. Why do they want you?"

He reached in his jacket pocket for his sonic before realising that River had never returned it to him. He grasped the rail in front of him.

"Is it Jack's DNA? Because he's immortal? Why did River want to lock you away in a Torchwood facility?" As expected, there was no response from the almost lifeless girl. "Dammit Amelia, why did you have to get yourself hurt?!"

The Doctor smacked the railing, only wincing slightly when pain shot up his arm. He moved to the side and sank down in Amy's vacated chair. 

"Dammit, Amelia," he repeated, softer this time, letting his head fall into his hands.

"Doc?" 

Jack inched his way into the room. He looked as if didn't want to be there. His eyes flicked everywhere, avoiding the still body on the hospital bed. 

"The Sisters know how to save her. But it's risky."

"You can't give her your heart, Jack. There's no way of knowing what it would do to you. Or to her,” the Doctor stated, voice flat.

"This isn't up to you."

"And what do you know about Time Lord DNA, Jack?" The Doctor stood up forcefully and faced the ex-time agent face on. "Your heart could end up killing her just as easily."

Jack stared him down. His fists were clenched painfully tight. There was silence for a moment, the steady whirs and beeps of Lia's machines the only sound in the room. 

"Where's River?" The Doctor spoke first, breaking the silence. 

"On the TARDIS." Defeat laced Jack's voice.

The Doctor brushed past him, determination spread across his face. Jack turned to watch him leave.

"You can't stop me if it's the only way, Doctor."

-

"I'm not letting Jack give up his heart."

The Doctor stormed into the TARDIS library to find River sat on the floor, waist deep in books.

"Well at least we agree on one thing, Sweetie," River replied, not looking up from her notes. 

"I'm serious..." He trailed off. "Wait, what?"

River sighed. She dragged her hair back from her face and used a hair tie to pull it into a messy pony tail. She moved some of the books from one pile to another, looked at her notes and sighed again. She looked tired, he noted. Not the kind of tired you got from not having enough sleep, but the look of someone who had been through too much.

"Mixing Jack's immortal DNA with Lia's Time Lord DNA would not be a clever thing to do," River answered him, indicating the pile of Gallifreyan books to her left. "Her body's enough of a volatile mess as it is."

She made to get up and smiled in surprise when the Doctor offered her a hand. She grabbed it and he pulled her to him. 

"Surely their DNA is already mixed?"

"What?" River frowned. 

"I heard you talking to Jack earlier, River. I know he's Lia's father."

Whatever the Doctor expected River's response to be, it definitely wasn't the burning sensation on his cheek that suggested she'd slapped him. Again.

"You can be a right _idiot_ sometimes, Sweetie," she bit out the endearment, eyes narrowed. 

River turned to grab her notes and stormed from the Library, ignoring the Doctor's frustrated and confused calling of her name. 

-

Cheek still stinging, he made his way to one of the many kitchens situated on the TARDIS. As soon as he entered he tried to leave again when he spotted the Ponds.

"Oh no you don't," Amy called out as she spotted him.

The Doctor forced a smile onto his face, spinning round and clapping his hands.

"Ah, Ponds. Didn't see you there."

Rory rolled his eyes. Amy grabbed the Doctor by his sleeve and dragged him into one of the chairs.

"What have you done now?" She questioned him. 

"I...what?" 

"River's angry and you've got a large red mark on your cheek. It's not that difficult to figure out," Rory deadpanned. 

"I may have accidentally insinuated that I knew Jack was Lia's father..."

Rory rolled his eyes again, this time accompanied by Amy face palming. She smacked the back of the Doctor's head with her other hand.

"You are an idiot," she stated firmly, ignoring his indignant outburst. "A bloody idiot."

The Doctor rested his arms on the table and dropped his forehead onto them. He groaned.

"I'm so stupid. Thick." He banged his head on his arms at every syllable. "Too old, too stupid. Jack's not her father is he?"

He raised his head slightly to come face to face with a bemused Amy Pond and a smirking centurion. He let his head fall back down again with a second groan. 

“I’m an idiot.”


	4. Chapter 4

**Notes for the Chapter:**

> I'm not a fan of this chapter. I edited bits here and there but I'm lazy and didn't want to entirely rewrite something I wrote I don't know how many years ago. Anyway, hope it's still enjoyable.

The Doctor paused in front of the study door, hand on the door handle. He needed to confront River about everything. He was about to push down on the handle when something made him stop. Voices were coming from inside the room; River was talking to someone.

The Doctor pressed himself close to the door, ear against the wood. 

"I can't do this." He could just make out River's voice. It was muffled through the door, but he could still hear how choked up she sounded. The sound of someone who was refusing to cry. His heart constricted at the thought.

"Yes you can, my love. You're the strongest person I know." 

The Doctor backed away from the door in horror. That was _his_ voice. But it wasn't _him_. No, he was stood outside the study. That was another him. A future him. _River's_ him.

Slowly and carefully, he made his way back to his position at the door. Spoilers be damned, he was going to listen to this conversation - ignoring the rather obvious fact that his future self would know he was eavesdropping. 

"He doesn't know anything. Can't you stay? I need you. Lia needs you. I'm pretty sure even Jack needs you right now." 

"I'm sorry, River. But you know I _can't_ ," his voice caught on the last word. The Doctor could tell that future him really did want to stay. "Believe me when I say this will all turn out alright."

River gasped softly. "You mean she'll be okay?"

The Doctor could almost hear the future him grimace. "She'll be fine, in the end. And so will you. But things will get worse, a lot worse, before they get better."

"What about spoilers?" 

"I think under the circumstances I'm allowed to break my own rule." The future Doctor laughed. "Come here." 

The Doctor could only guess that they were hugging. Or kissing. He found himself blushing at the thought. He also found himself slightly jealous of the future him, which was utterly ridiculous. 

"I'm sorry." The Doctor could only just make out what the other him was saying, voice muffled by what he suspected was River's hair.

"It's not your fault, Sweetie." 

"No, I'm sorry for him. He's an arse, River. But he gets better. I promise." They were talking about him. The current him. He bit his lip as he realised just how badly he'd been treating River.

The future him whispered something incomprehensible to River and then there was a large crackle of static. Suddenly the door opened in front of him. 

"Sweetie, did no one ever tell you that eavesdropping is rude?" River said, her eyes not betraying her emotions. 

"I..." The Doctor stood up straight, changing the topic to the vortex manipulator. "Since _when _did I ever willingly use that ridiculous mode of transport."__

__River's eyes widened slightly and gained a far off misty look to them. The corners of her mouth turned down into a frown._ _

__"Since the TARDIS got destroyed," River answered softly, voice thick with emotion._ _

__The Doctor's eyes widened in horror, his body temperature increased and his hearts rates doubled. There was a pause. River smirked, only just stopping herself from bursting into laughter. The Doctor narrowed his eyes and glared._ _

__"You're incorrigible, River Song," he huffed. “That wasn’t funny.”_ _

__"Since," she paused, the smirk still gracing her features. "Spoilers."_ _

__All the air seemed to drain from him. He sighed and grabbed both of River's hands with his own._ _

__"I'm sorry for being...for being this."_ _

__River avoided his gaze and lowered her head. The Doctor could only just see the small smile that graced her lips._ _

__"I'm an idiot, River. A stupid, old man. And I'm sorry for everything."_ _

__"Oh, Honey." She looked up, freeing one of her hands from his and straightening his bowtie fondly. "You really are an idiot, but you're _my_ idiot."_ _

__"River!" River snapped her head to the side as Amy came running down the corridor. "River, she's gone."_ _

__"What?" Amy stopped in front of them and grabbed River's arm._ _

__"Lia," she said, out of breath, pulling River with her. "She's gone. She's not there anymore."_ _

__River took one look at the Doctor and then took off down the corridor, Amy following close behind her._ _

__The Doctor followed at a distance, hearts pounding with worry. He stumbled to a halt when he entered the control room. River and Amy had just vanished outside the TARDIS doors when the scanner starting fizzing. He bounded over to the console, grabbing the scanner and hitting it a few times._ _

__"What are you trying to tell me, girl?" He asked the TARDIS._ _

__The scanner flared red for a moment before lines of binary code began scrolling up the screen. It was a new form of the signal that had been tracking Lia. Except this time, the signal was a message. The Doctor typed commands into the keyboard and when a single line of code flashed up. He didn't need it to be translated to read it, but the TARDIS did so anyway. He hit the console in anger before turning to leave._ _

__The TARDIS door slammed shut behind him, leaving three large words flashing blue on the scanner's screen._ _

___Silence will fall._ _ _

__-_ _

__When the Doctor reached Lia's hospital room, he instantly felt the tension in the air. Amy and Rory were stood on either side of River, a hand each in hers. Whether it was in comfort or restraint, the Doctor couldn't tell. Jack was opposite them, face pale in worry and fear. Worry for Lia, fear of River._ _

__"Someone was meant to be watching her at all times!" River was yelling._ _

__"I know. I'm sorry. You _know_ I'm sorry." Jack's face paled even more._ _

__"God _damn_ it, Jack."_ _

__"I know who took her." Only River didn't jumped at his sudden appearance._ _

__River turned to him and the Doctor actually took a step back as he noticed the pure fury in her eyes._ _

__"Who?"_ _

__He swallowed heavily. "The Silence."_ _

__Amy gasped and Rory's hand tightened around River's. Jack swore before mumbling more apologies in River’s direction. River just closed her eyes tightly and inhaled sharply. The Doctor could tell she was trying to hold back the tears in front of them all; he felt a part of him break at the sight of her._ _

__"Can you trace them?" Rory asked._ _

__"I...I don't know."_ _

__"Try." His voice hardened, the Centurion part of him showing itself._ _

__The Doctor nodded. Everyone rushed into the TARDIS ignoring the elephant in the room. If being treated by the Sisters of the Infinite Schism was all that was keeping Lia alive, just how long did she have left?_ _

__-_ _

__"Do you all have to hover around me? I'm trying to be really clever here," the Doctor huffed._ _

__"I thought you liked people witnessing your cleverness." Amy glared at him._ _

__"Right, working." The Doctor gulped before typing more commands into the keyboard below the scanner. "I should be able to trace the message they left us back to its original source. But it's buried under a lot of useless stuff."_ _

__River was stood on the opposite side of the time rotor, ignoring everyone. She'd hooked her handheld computer up to the TARDIS console and was using one of her hacking algorithms to wirelessly enter the computer that had left the message on the TARDIS scanner._ _

__Amy, Rory and Jack stood together, watching the two work. Worry flooded through Amy as she thought about what could be happening to her granddaughter. Kovarian took her daughter from her, she wasn't allowed to do the same thing to River. Amy's face hardened. Rory squeezed her hand as if he knew exactly what was going through her mind. The same thoughts were probably going through his._ _

__"Got it!" Both River and the Doctor exclaimed at the same time._ _

__"She's somewhere in the Virgo Cluster." The Doctor beamed, proud of his own intelligence. "We'll have to get closer before I can pinpoint where."_ _

__"She's not in the Virgo Cluster." River rolled her eyes. "She's on the edge of the Tri System."_ _

__The Doctor scoffed and moved to look over River's shoulder._ _

__"You didn't calculate for interstellar drift," he huffed._ _

__"And you, _Honey_ ," she said, moving to the scanner. "Didn't calculate for temporal shift."_ _

__They looked at each other and something clicked into place. Frantically they moved together, typing in commands to both the console and River's handheld._ _

__"What?" Amy asked._ _

__"We're both stupid," the Doctor yelled, a bright smile on his face. "The Silence used two signals to send the message. The signals were mixed together and sent from three different planets."_ _

__"If we cross reference the two places the Doctor and I found, we should get the third. That'll be where Lia is," River explained._ _

__The scanner pinged. The Doctor grinned triumphantly and even River had to offer up a small smile at his enthusiasm. Both of them danced around the TARDIS, pulling her into the time vortex and towards where the Silence had taken Lia._ _


	5. Chapter 5

The TARDIS materialised, silent and invisible, in a dark corridor. River was the first out of the doors, gun out of its holster. Jack followed, his own pistol gripped tightly in his hand. Amy and Rory, much to their anger and protest, had been forced to stay behind. The Doctor was the last out the TARDIS, locking the doors behind him, knowing Amy and Rory's tendency to blatantly ignore his demands for them to stay safe. 

River grabbed the Doctor's sonic screwdriver with her free hand and passed it back to him. He still refused to carry a gun, so the sonic would have to do. 

River and Jack were both decked out in black combat gear; the Doctor had refused and was wearing the usual tweed, braces and bowtie combo. The threesome made their way through the base. The Doctor, with River and Jack's help, had hacked into the computer systems when they landed and the downloaded blueprints were now glaring on the screen of River's handheld. The corridors were suspiciously deserted. Slowly they made their way to the base's operation room. 

The two guards and five technicians were dead before the Doctor could blink. He clenched his jaw angrily, but remained silent. River – backed by Jack – hadn’t listened to a word he’d said about avoiding unnecessary deaths. 

Jack quickly found his way into the computer's database whilst River stood guard at the door. The Doctor sort of hovered nervously between them.

"Sweetie, if you want, you can go back to the TARDIS," River offered, not really wanting him to see her kill anyone who got in her way and knowing he really didn't want to see it either. 

The Doctor looked up from where he'd briefly been looking over Jack's shoulder and walked over to her.

"I can't not help you. She's your daughter.” He smiled gently and River’s face softened.

“I guess," River smiled sadly. "I guess all this explains why you weren’t surprised when I told you I was pregnant.”

The Doctor froze at that. “River, who’s Lia’s father?”

Jack looked over his shoulder. Both he and River looked uncomfortable. River shot Jack a glance before replying to the Doctor’s question.

“You know I can’t tell you that. Your rules.” 

The Doctor's jaw clenched for the second time but he nodded and let the topic drop. The computer beeped suddenly and Jack span round, a triumphant grin on his face. 

"Got her. Uploading her position to your handheld now." The device flashed as it updated the base blueprints. "So, what's the plan?"

-

They were positioned on the walkways above a large room. The door to Lia's cell like room was beneath Jack. The Doctor was next to a power control box and River was opposite him.

River nodded from across the room and the Doctor soniced the power. The lights flickered off. Chaos erupted. The Church soldiers shouted, flashlights switched on and scanned the room, alarms blared. But it was too late.

River had jumped down from her perch and taken out five of them in the first two seconds. Jack followed suit, taking out two from where he was crouched on the walkway above them. The Doctor jumped down the stairs, running as fast as he could without falling over. He reached the ground floor just as a soldier fell to the ground in front of him. Dead. The Doctor winced. 

He looked up, and stared. 

She was like a dancer, he mused, watching River take out the enemy soldiers. He was fascinated by her movements, so much so that it took Jack calling out his name to snap him out of his trance. 

"Right. Right," he muttered to himself.

The Doctor made his way around the edge of the room, dodging the falling bodies with a grimace on his face.

"Any time now, Sweetie," River yelled, not even sounding out of breath. 

He reached the door to Lia's 'cell' and waved his screwdriver over it. His eyebrows raised in surprised as the lock flickered green. It only had a simple locking mechanism and with a flick of his wrist the door slid open. The Doctor ducked inside the room, looking up to find himself facing the barrel of a gun.

"Doctor." Kovarian's voice crawled over him.

"Madam Kovarian." The Doctor plastered a fake smile on his face. 

Outside the cell, he could still hear the sound of gunfire as more troops rushed into the room. Oddly, he seemed to care more about River's welfare than his own, regardless of the fact that she could handle herself a lot better than he could.

His eyes flicked from the gun in front of him to the deathly pale girl shackled to a hospital gurney. The Doctor's eyes narrowed and he turned back to look at Kovarian. 

"You failed with River. What did you expect to achieve by taking Lia?" He asked, voice dangerously low.

Kovarian laughed. "Oh this isn't just about _you_ , Doctor."

Gun still pointed at him, she moved behind the gurney to put Lia between them.

"This is about punishing Melody Pond."

The Doctor felt the familiar rage bubble up inside him. He took a step towards Kovarian but she smirked and shifted her aim. The gun was now directly pointed at Lia's head. The Doctor stopped moving, anger flooding through him.

River and Jack were still holding the soldiers back outside. The plan was all falling apart. They were all meant to be out of here now, safely on the TARDIS with Lia. Kovarian had put a kink in their plans for an easy escape. 

"Jack, cover me!" He heard River shout.

A second later he felt her familiar presence behind him. 

"I came to see what was taking you so bloody long." Pure, undiluted fury thickened her voice. "But I can see you ran into a bitch of trouble."

Kovarian just smiled at River's joke. River's eyes flicked over to Kovarian's gun and the direction in which it was aimed, and her own gun flew up.

"Put it down." Kovarian raised an eyebrow. "You know I can kill you before your finger even twitches on the trigger, Madam Kovarian."

"Then why haven't you shot me already?" The woman laughed. "The woman who killed the Doctor. You could have been so much more."

River didn't move, didn't blink, didn't breathe. Her eyes were focused on the gun pointing at her daughter. 

"It's a shame we didn't get Amelia before now." She smiled knowingly at the Doctor. "The child of the Doctor. How much would worlds beg to have her. Think about what secrets her body contains."

River swallowed heavily, the only tell to her obvious discomfort. The Doctor's eyes widened as everything finally clicked together in his head, piece by agonising piece. 

"Amelia. Like a name in a fairytale," River whispered, quoting what he'd said to her mother all those years ago.

Something in the Doctor snapped at that. He pointed the sonic screwdriver at Kovarian. Fear glanced across her face just as the room went dark.

The lights flickered and River could barely make out the Doctor pinning Kovarian to the wall. His hand was round her throat. There was a clatter when Kovarian's gun dropped to the floor, the woman's strength weakening. She was gasping for breath, terror plastered on her face. 

"You take the child of my best friends," the Doctor growled. "And turn her into a weapon to use against me."

The pressure against Kovarian's throat increased, the rage in the Doctor's eyes burning brighter.

"Then you have the nerve, the _audacity_ , to take _my_ child. Because your 'weapon' didn't turn out quite as you planned."

River stood paralysed at the site of the Doctor. She knew the _Mighty Warrior_ , the _Oncoming Storm_ , she’d seen him at his best and at his worst, but never had she seen so much anger and hate displayed across his face. 

She caught Kovarian's movements a second too late and before she had time to react the woman vanished into thin air. The Doctor fell against the wall, unmoving. The smell of transporter energy fizzed around them.

River walked towards him and gently laid a hand on his shoulder, turning him to face her. Tears lined his eyes and she felt moisture well up in her own. Before she knew what was happening, the Doctor pulled her into a hug, burying his face in her hair. 

"They've gone." Jack ran into the room. "The soldiers have all gone."

He noticed the couple's embrace and coughed awkwardly. "Sorry."

River pulled away from the Doctor's arms and fondly wiped her thumb across his cheek. She smiled.

"Come on, Sweetie." 

The Doctor nodded and thumbed his screwdriver, unlocking the chains around Lia's wrist. Then he pressed it a second time. The air buzzed around them and the threesome found themselves inside the TARDIS' medical bay, the time ship having materialised around them. 

"That took you long enough. What happened?" Amy said.

"Kovarian." River's one word answer was enough. 

Amy gasped before grabbing her daughter roughly and pulling River in for a tight hug. Rory wrapped his arms around them both. The Doctor looked at his Ponds and his heart constricted, guilt working its way through his chest.

Suddenly, Lia gasped. Her body raising from the bed in agony. She'd been out of the care of the Sisters for too long and without whatever meagre medical care The Silence had been giving her, her body was finally shutting down.

"Doctor, do something!" Jack yelled as everyone looked on in shocked horror.

Without even thinking, the Doctor stepped forward, an orange glow forming around his hands. 

"Doctor, stop!" He ignored River's shouts and placed his hands against the deep wound on Lia's chest.

"Amy, hold her back," was all he said before regeneration energy flowed through him.

-

It had been two days since he'd used regeneration energy to heal his daughter. His daughter. He couldn't get his head around those two words. He had a daughter again; this time with River. Every day it seemed more and more likely that River was his wife, and every day he started to avoid the idea less. 

But since he’d saved Amelia, he'd been avoiding everyone. As soon as she had gasped back to life, he'd fled. The TARDIS was surprisingly on his side for once and had hidden his study somewhere that even River couldn't find. 

He had a family again, he realised with a smile. A proper family. The guilt of nearly killing Kovarian slowly washed away with the thought.

"She finally decided you were ready for company." River's voice made him jump.

She smiled and practically _sauntered_ over to him. He grinned.

"Doctor River Song. My bad, bad girl."

She sat on the arm of his chair and turned to face him. "Are you okay, Sweetie?"

He thought for a moment before nodding. His hand came up to rest on her knee. 

"I just needed time to think, you know?"

River nodded in understanding, a small smile forming on her lips. 

"Thank you. For saving her."

The Doctor's eyebrows rose in shock.

"Did you really think I wouldn't, River? She's our daughter." River's smile bloomed into a full grin at his words. 

“I’m sorry,” he spoke suddenly, his voice soft. “I get so wound up in the middle of it all sometimes, that I only think about myself. I forget that you're only abiding by my rules.”

The atmosphere of the room changed at his words. She looked away from him but he still noticed the sadness appearing in her eyes. The Doctor grabbed her arm and pulled River onto his lap. She yelped in surprise, but made no move to leave her new found position. . They sat in silence for a moment before River spoke. 

“You’re starting to get too young,” she murmured into his shoulder. “I’m losing you.”

The Doctor’s hearts clenched unbearably in his chest, his memory painfully reminding him of The Library, and he suddenly realised what he’d been pushing away for far too long. He pulled River tighter against him.

“I will always love you, River,” he whispered into her hair. “I just might not always know it.”

“I hate it. This. I hate it.”

“Time can be rewritten…”

“Don’t you dare,” she growled, smiling into his chest despite herself.

The Doctor smiled against the top of River’s head. 

“How long…?” She trailed off quietly.

The Doctor faltered for a moment before replying.

“Deep down, I think I’ve been falling since I met you. But it was Berlin where I started trying to push it away. You’re magnificent River Song, even when you don’t know it.”

River looked up at him before resting her forehead against his cheek. She sighed. 

“You’re ridiculous, you know that?”

“Mad man in a box.” He grinned at her, brushing a curl from her face. "I mean it River, I love you."

"I love you too, Sweetie."

And with that, she threaded her hands through his hair and kissed him.

**Notes for the Chapter:**

> And there we have it. I hope you guys enjoyed this fic. I still can't believe I never posted it all those years ago, but here we are now. Thank you to everyone who has read it, kudos'd it, or commented on it.


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